MacroModel Reference Manual - ISP

Chapter 4: Operation CodesLMC2 is implemented to extend the basic use of LMCS to molecules of virtually any size. Notethat two main features of LMCS, LMCS-SHAKE and LMCS mode-following, are not implementedin LMC2. The command arguments of LMC2 are fairly similar to those of LMCS. LikeLMCS, LMC2 can also be used in conjunction with the MCMM command to explicitly alter keytorsion bonds via TORS commands (with RCA4 to open macrocyclic structures if necessary)and apply explicit translation/rotation of a ligand with the MOLS command for docking. LMC2 isprimarily designed for fully flexible molecules, but the use of frozen atoms is allowed, andrecommended in cases where parts of a macromolecule can be treated rigidly. Also note thatyou can set certain parameters controlling the ARPACK package via the ARPK command.The AUTO opcode can be used for automatic setup of LMC2 and MCMM/LMC2 calculations. It canbe used for MCMM/LMC2 serial searches but not for pure LMC2 serial searches.LMCS is more efficient than LMC2 when the number of atoms is small enough for the entireHessian to be stored in computer memory without swapping.Note:Note:arg1It has proven to be good practice and time-saving to minimize molecular structuresduring a conformational search to a gradient that is not too low and only re-minimizeentirely the final set of low-energy conformations. In that respect, LMC2 needs specialattention. It is still recommended to follow this scheme, e.g., for unconstrainedproteins, a gradient RMS of 1 kJ/mol/Å is sufficient during the search, but the very firststructure, for which the low-modes are computed, must be pre-minimized to a low,< 0.1 kJ/mol/Å gradient RMS in order to derive reasonable modes. Pre-minimizationcan either be done in a separate MacroModel job, or the RWND command can be usedto fully minimize the first structure, rewind the output file and start the LMC2 conformationalsearch from there.Large-scale low-mode calculations can use a large amount of memory. If memoryissues are encountered, consider eliminating the use of solvation. In addition, reducingnon-bonded cutoffs also reduces the memory required for the computation.Number of Monte Carlo steps to be carried out before stopping0 Carry out the search until arg2 structures have been found. We do not recommendthe use of this default.arg2Maximum number of structures to retain while running0 The maximum number of conformations to retain while running is the value specifiedin arg1 or 10,000, whichever is greater.>0 This is the maximum number of conformations to retain while running.MacroModel 9.7 Reference Manual 91